Mercurial > repos > xuebing > sharplabtool
view tools/emboss_5/emboss_format_corrector.py @ 1:cdcb0ce84a1b
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author | xuebing |
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date | Fri, 09 Mar 2012 19:45:15 -0500 |
parents | 9071e359b9a3 |
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#EMBOSS format corrector import operator #from galaxy import datatypes #Properly set file formats after job run def exec_after_process( app, inp_data, out_data, param_dict,tool, stdout, stderr): #Properly set file formats before job run #def exec_before_job(trans, inp_data, out_data, param_dict,tool): #why isn't items an ordered list? items = out_data.items() #lets sort it ourselves.... items = sorted(items, key=operator.itemgetter(0)) #items is now sorted... #normal filetype correction data_count=1 for name, data in items: outputType = param_dict.get( 'out_format'+str(data_count), None ) #print "data_count",data_count, "name", name, "outputType", outputType if outputType !=None: if outputType == 'ncbi': outputType = "fasta" elif outputType == 'excel': outputType = "tabular" elif outputType == 'text': outputType = "txt" data = app.datatypes_registry.change_datatype(data, outputType) app.model.context.add( data ) app.model.context.flush() data_count+=1 #html filetype correction data_count=1 for name, data in items: wants_plot = param_dict.get( 'html_out'+str(data_count), None ) ext = "html" if wants_plot == "yes": data = app.datatypes_registry.change_datatype(data, ext) app.model.context.add( data ) app.model.context.flush() data_count+=1 #png file correction data_count=1 for name, data in items: wants_plot = param_dict.get( 'plot'+str(data_count), None ) ext = "png" if wants_plot == "yes": data = app.datatypes_registry.change_datatype(data, ext) app.model.context.add( data ) app.model.context.flush() data_count+=1